Research workbench
Leucyl-tRNA synthetase from thermus thermophilus complexed with a sulphamoyl analogue of leucyl-adenylate in the synthetic site and an adduct of AMP with 5-fluoro-1,3- dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site
Analyse Leucyl-tRNA synthetase from thermus thermophilus complexed with a sulphamoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V0C
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoacyl-tRNA synthetase
- UniProt
- Q7SIE4
- Ligands
- LEU, LMS, ANZ, ZN, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoacyl-tRNA synthetase | protein | 810 | 43% helix, 20% strand | Q7SIE4 |
Ligands and binding sites
- LEU · Leucine · ligand · chains A
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · chains A
- ANZ · [(6-amino-9H-purin-9-yl)-[5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole]-4'yl]methyl dihydrogen phosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.73 | 0.79 | 66 | LEU, LMS |
| 2 | 392 | 0.66 | 0.79 | 38 | ANZ |
| 3 | 60 | 0.34 | 0.77 | 13 | empty |
| 4 | 105 | 0.34 | 0.73 | 19 | empty |
| 5 | 68 | 0.32 | 0.75 | 16 | empty |
Compared structures
- 2V0C · LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7SIE4
- Elsewhere: RCSB PDB 2V0C · PDBe 2V0C · UniProt Q7SIE4
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